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- PDB-2e2a: ASP81LEU ENZYME IIA FROM THE LACTOSE SPECIFIC PTS FROM LACTOCOCCU... -

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Basic information

Entry
Database: PDB / ID: 2e2a
TitleASP81LEU ENZYME IIA FROM THE LACTOSE SPECIFIC PTS FROM LACTOCOCCUS LACTIS
ComponentsPROTEIN (ENZYME IIA)
KeywordsTRANSFERASE / ENZYME IIA / HELICAL BUNDLES / PTS / PHOSPHOTRANSFERASE SYSTEM
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / metal ion binding / cytoplasm
Similarity search - Function
Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 domain profile. / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PTS system lactose-specific EIIA component
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsSliz, P. / Koch, B. / Hengstenberg, W. / Pai, E.F.
Citation
Journal: To be Published
Title: Structure of Asp81Leu Enzyme Iia from the Lactose Specific Pts from Lactococcus Lactis
Authors: Sliz, P. / KOCH, B. / Hengstenberg, W. / Pai, E.F.
#1: Journal: Structure / Year: 1997
Title: The Structure of Enzyme Iialactose from Lactococcus Lactis Reveals a New Fold and Points to Possible Interactions of a Multicomponent System
Authors: Sliz, P. / Engelmann, R. / Hengstenberg, W. / Pai, E.F.
History
DepositionMay 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ENZYME IIA)
B: PROTEIN (ENZYME IIA)
C: PROTEIN (ENZYME IIA)


Theoretical massNumber of molelcules
Total (without water)34,3843
Polymers34,3843
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-47 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.960, 87.960, 79.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.1092, -0.0558, 0.9925), (0.9867, -0.1147, -0.115), (0.1202, 0.9918, 0.0426)30.3671, -20.0251, -14.4847
2given(0.0475, 0.9912, 0.1235), (-0.0491, -0.1212, 0.9914), (0.9977, -0.0531, 0.0429)21.4629, 14.0346, -32.1617
3given(0.0738, -0.0813, 0.994), (0.9854, -0.1475, -0.0852), (0.1535, 0.9857, 0.0692)31.9729, -20.0692, -16.0618

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Components

#1: Protein PROTEIN (ENZYME IIA) / ENZYME III / LACTOSE-SPECIFIC IIA COMPONENT


Mass: 11461.188 Da / Num. of mol.: 3 / Mutation: D81L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: MG1820 / Description: NIZO, NETHERLANDS / Gene: LACF / Production host: Escherichia coli (E. coli)
References: UniProt: P23532, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 44.56 %
Crystal growpH: 6.5
Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.9M NA ACETATE AND 0.1M NA CACODYLATE AT PH 6.5. HANGING-DROP METHOD WAS USED. THE INITIAL CONCENTRATION OF THE PROTEIN IN THE DROP WAS 5 MG/ML.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.949
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 2.1→36 Å / Num. obs: 18726 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.037 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.271 / % possible all: 99.9

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Processing

Software
NameClassification
MOSFLMdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: 1E2A

1e2a


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1666967.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1836 9.8 %RANDOM
Rwork0.198 ---
obs-18682 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.47 Å2 / ksol: 0.3684 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2--2.58 Å20 Å2
3----5.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 173 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.176
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.831.5
X-RAY DIFFRACTIONc_mcangle_it3.732
X-RAY DIFFRACTIONc_scbond_it4.622
X-RAY DIFFRACTIONc_scangle_it6.322.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 278 9.1 %
Rwork0.226 2763 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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